Minor updates (possibility to specify custom server port and temporar…

…y result folder) > Version 3.4
fra82 · May 4, 2020 · 2508256 · 2508256
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diff --git a/pom.xml b/pom.xml
@@ -247,5 +247,5 @@
 	</dependencies>
 
 
-	<version>3.3</version>
+	<version>3.4</version>
 </project>
diff --git a/rtdoc/LocalExecution.md b/rtdoc/LocalExecution.md
@@ -6,9 +6,9 @@
 Comorbidity4j has to be executed by Java 1.8 or newer. As a consequence, as a prerequisite for the execution of Comorbidity4j you need to have <a href="https://www.java.com/en/download/" target="_blank">Java</a> installed.  
 
 ## Download the JAR package 
-The compressed archive (comorbidity4j-3.3-bin.zip) that contains the latest version (LATEST_VERS = 3.3) of comorbidity4j can be downloaded at the following URL:  
+The compressed archive (comorbidity4j-3.4-bin.zip) that contains the latest version (LATEST_VERS = 3.4) of comorbidity4j can be downloaded at the following URL:  
 
-<a href="https://github.com/fra82/comorbidity4j/releases/tag/3.3" target="_blank">https://github.com/fra82/comorbidity4j/releases/tag/3.3</a>    
+<a href="https://github.com/fra82/comorbidity4j/releases/tag/3.4" target="_blank">https://github.com/fra82/comorbidity4j/releases/tag/3.4</a>    
 
 
 ## Comorbidity4j Execution  
@@ -18,14 +18,43 @@ The compressed archive (comorbidity4j-3.3-bin.zip) that contains the latest vers
 
 ```
 // Linux users:  
-java -cp './comorbidity4j-LATEST-VERS.jar:./lib/*' es.imim.ibi.comorbidity4j.server.StartComorbidity4j  
+java -cp '/local/path/to/comorbidity4j-LATEST-VERS/comorbidity4j-LATEST-VERS.jar:/local/path/to/comorbidity4j-LATEST-VERS/lib/*' es.imim.ibi.comorbidity4j.server.StartComorbidity4j  
     
 // Windows users:  
-java -cp "c:\Full\Local\Path\To\comorbidity4j-LATEST-VERS\comorbidity4j-LATEST-VERS.jar;c:\Full\Local\Path\To\comorbidity4j-LATEST-VERS\lib\*" es.imim.ibi.comorbidity4j.server.StartComorbidity4j  
+java -cp "c:\Local\Path\To\comorbidity4j-LATEST-VERS\comorbidity4j-LATEST-VERS.jar;c:\Local\Path\To\comorbidity4j-LATEST-VERS\lib\*" es.imim.ibi.comorbidity4j.server.StartComorbidity4j  
 ```  
 
 + Open by your favorite Web browser the URL: <a href="http://localhost:8181/comorbidity4web/" target="_blank">http://localhost:8181/comorbidity4web/</a>. Here you can access the Web interface that will drive you throughout the different step and the exploration of results of a comorbidity analysis. The same Web interface can be accessed at <a href="http://comorbidity.eu/comorbidity4web/" target="_blank">http://comorbidity.eu/comorbidity4web/</a> as the COmorbidity4web service, for online execution of comorbidity analyses.  
 
++ Specify custom server port and temporary files directory path:  
+To change default server port (8181), when starting comorbidity4j local service (server), specify the following program parameter:  
+
+```  
+--server.port=8585  
+```  
+
+To change the temporary files directory path (the local directory where Comorbidity4web writes partial and final resulta of comorbidity analyses), when starting comorbidity4j local service (server), specify the following program parameter:  
+
+```  
+// Linux users:  
+--spring.servlet.multipart.location=/path/to/temporary/files/directory/  
+  
+// Windows users:  
+--spring.servlet.multipart.location=c:\local\path\to\temporary\files\directory\  
+```  
+
+
+To specify a custom server port or temporary files directory path, start the server with the following program parameters:  
+```  
+// Linux users:  
+java -cp '/local/path/to/comorbidity4j-LATEST-VERS/comorbidity4j-LATEST-VERS.jar:/local/path/to/comorbidity4j-LATEST-VERS/lib/*' es.imim.ibi.comorbidity4j.server.StartComorbidity4j  
+     --server.port=PORT_NUMBER --spring.servlet.multipart.location=/path/to/temporary/files/directory/  
+  
+// Windows users:  
+java -cp "c:\Local\Path\To\comorbidity4j-LATEST-VERS\comorbidity4j-LATEST-VERS.jar;c:\Local\Path\To\comorbidity4j-LATEST-VERS\lib\*" es.imim.ibi.comorbidity4j.server.StartComorbidity4j  
+     --server.port=PORT_NUMBER --spring.servlet.multipart.location=c:\local\path\to\temporary\files\directory\  
+```  
+
 
 <a name="results"></a>  
 

diff --git a/rtdoc/index.md b/rtdoc/index.md
@@ -1,7 +1,7 @@
 ![Comorbidity4j](/img/logo.png)
 <h3>Open-source Java tool to analyze comorbidities over large datasets of patients</h3>
 
-**Latest version: 3.3**
+**Latest version: 3.4**
 
 Comorbidity4j is an Open-source java tool tailored to easily perform <a href="https://en.wikipedia.org/wiki/Comorbidity" target="_blank">comorbidity analyses</a>, thus **supporting the analysis of significant cooccurrences of diseases over large datasets of patient data**.  
 

diff --git a/src/main/java/es/imim/ibi/comorbidity4j/server/StartComorbidity4j.java b/src/main/java/es/imim/ibi/comorbidity4j/server/StartComorbidity4j.java
@@ -1,12 +1,16 @@
 package es.imim.ibi.comorbidity4j.server;
 
+import java.io.File;
 import java.util.Arrays;
 
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
+import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.context.annotation.Bean;
+import org.springframework.core.env.Environment;
 import org.springframework.scheduling.annotation.EnableScheduling;
 
 import es.imim.ibi.comorbidity4j.server.reservlet.ComputeComorbidityServlet;
@@ -17,11 +21,109 @@
 // @EnableAutoConfiguration
 @EnableScheduling
 public class StartComorbidity4j extends SpringBootServletInitializer {
-
+	
 	public static void main(String[] args) {
-		SpringApplication.run(StartComorbidity4j.class, args);
+
+		final ConfigurableApplicationContext context = SpringApplication.run(StartComorbidity4j.class, args);
+		StartComorbidity4j c4j = context.getBean(StartComorbidity4j.class);
+
+		System.out.println("-------------------------------------------------");
+		System.out.println("\n--- SERVER STARTUP CONFIGURATION GUIDE ---");
+		System.out.println("-   To change server port:\n-       when you start Comorbidity4j server, specify the following program parameter: --server.port=8585");
+		System.out.println("-   To change temporary files directory path:\n-       when you start Comorbidity4j server, specify the following program parameter: --spring.servlet.multipart.location=/path/to/temporary/files/directory/");
+		System.out.println("-\n-   To start the server:");
+		System.out.println("-      > Linux users:");
+		System.out.println("-        java -cp '/local/path/to/comorbidity4j-LATEST-VERS/comorbidity4j-LATEST-VERS.jar:/local/path/to/comorbidity4j-LATEST-VERS/lib/*' es.imim.ibi.comorbidity4j.server.StartComorbidity4j");
+		System.out.println("-      > Windows users:");
+		System.out.println("-        java -cp \"c:\\Local\\Path\\To\\comorbidity4j-LATEST-VERS\\comorbidity4j-LATEST-VERS.jar;c:\\Local\\Path\\To\\comorbidity4j-LATEST-VERS\\lib\\*\" es.imim.ibi.comorbidity4j.server.StartComorbidity4j"); 
+		System.out.println("-\n-   To specify a custom server port or temporary files directory path, start the server with the following program parameters:");
+		System.out.println("-      > Linux users:");
+		System.out.println("-        java -cp '/local/path/to/comorbidity4j-LATEST-VERS/comorbidity4j-LATEST-VERS.jar:/local/path/to/comorbidity4j-LATEST-VERS/lib/*' es.imim.ibi.comorbidity4j.server.StartComorbidity4j");
+	    System.out.println("-	         --server.port=PORT_NUMBER --spring.servlet.multipart.location=/path/to/temporary/files/directory/");
+		System.out.println("-      > Windows users:");
+		System.out.println("-        java -cp \"c:\\Local\\Path\\To\\comorbidity4j-LATEST-VERS\\comorbidity4j-LATEST-VERS.jar;c:\\Local\\Path\\To\\comorbidity4j-LATEST-VERS\\lib\\*\" es.imim.ibi.comorbidity4j.server.StartComorbidity4j");
+	    System.out.println("-	         --server.port=PORT_NUMBER --spring.servlet.multipart.location=c:\\local\\path\\to\\temporary\\files\\directory\\");
+	    System.out.println("-------------------------------------------------"); 
+
+		System.out.println("\n------------------- COMORBIDITY4WEB SERVER -------------------");
+		// Check if the temp directory exists and is writable
+		boolean startupCheckPassed = true;
+		try {
+			System.out.println(" --> Checking running port number:");
+			if(c4j.getEnv() == null || !c4j.getEnv().containsProperty("server.port") || c4j.getEnv().getProperty("server.port") == null) {
+				System.out.println(" >>> ATTENTION: wrongly specified server port number.");
+				startupCheckPassed = false;
+			}
+			else {
+				System.out.println("   Server port number equal to: " + c4j.getEnv().getProperty("server.port"));
+			}
+		}
+		catch(Exception e) {
+			e.printStackTrace();
+		}
+
+		try {
+			System.out.println(" --> Checking the validity of the temporary files directory path (the local directory where Comorbidity4web writes partial and final resulta of comorbidity analyses):");
+
+			if(c4j.getEnv() == null || !c4j.getEnv().containsProperty("spring.servlet.multipart.location") || c4j.getEnv().getProperty("spring.servlet.multipart.location") == null) {
+				System.out.println(" >>> ATTENTION: the temporary files to directory path property is not specified.");
+				startupCheckPassed = false;
+			}
+			else {
+				File tempDir = new File(c4j.getEnv().getProperty("spring.servlet.multipart.location"));
+				if(tempDir == null || !tempDir.exists()) {
+					System.out.println(" >>> ATTENTION: the temporary files to directory path points to a directory that does not exist.");
+					startupCheckPassed = false;
+				} 
+				else if(!tempDir.isDirectory()) {
+					System.out.println(" >>> ATTENTION: the temporary files directory path points to local file system location that is not a directory.");
+					startupCheckPassed = false;
+				}
+				else if(!tempDir.canWrite()) {
+					System.out.println(" >>> ATTENTION: the server is not allowed to write files in the the temporary files directory path.");
+					startupCheckPassed = false;
+				}
+				else {
+					System.out.println("   Temporary files directory path correctly specified and equal to: " + c4j.getEnv().getProperty("spring.servlet.multipart.location"));
+					ComputeComorbidityServlet.basePathResultStorage = c4j.getEnv().getProperty("spring.servlet.multipart.location");
+					ComputeComorbidityServlet.basePathResultStorage = (ComputeComorbidityServlet.basePathResultStorage.endsWith(File.separator)) ? ComputeComorbidityServlet.basePathResultStorage : ComputeComorbidityServlet.basePathResultStorage + File.separator;
+				}
+			}
+		}
+		catch(Exception e) {
+			e.printStackTrace();
+		}
+
+		if(startupCheckPassed) {
+			System.out.println("\n--- SERVER CONFIGURATION ---");
+			System.out.println("- Server port: " + ((c4j.getEnv() != null && c4j.getEnv().containsProperty("server.port") 
+					&& c4j.getEnv().getProperty("server.port") != null) ? c4j.getEnv().getProperty("server.port") : "UNAVAILABLE"));
+			System.out.println("- Temporary files directory path (local directory where Comorbidity4web writes partial and final resulta of comorbidity analyses): " + ((c4j.getEnv() != null && c4j.getEnv().containsProperty("spring.servlet.multipart.location") && 
+					c4j.getEnv().getProperty("spring.servlet.multipart.location") != null) ? c4j.getEnv().getProperty("spring.servlet.multipart.location") : "UNAVAILABLE"));
+
+			System.out.println("\nComorbidity4web server can be accessed at the following URL: http://localhost:" + c4j.getEnv().getProperty("server.port") + "/comorbidity4web/");
+		}
+		else {
+			System.out.println(" >>>            Please, stop the server, solve this issue and restart the server.");
+		}
+
+		System.out.println("\n >>>            Documentation: https://comorbidity4j.readthedocs.io/");
+		System.out.println("----------------------------------------------------------------");
+
+
+
+	}
+
+	@Autowired
+	private Environment env;
+
+	public Environment getEnv() {
+		return env;
 	}
 
+	public void setEnv(Environment env) {
+		this.env = env;
+	}
 
 	@Bean
 	ServletRegistrationBean<ComputeComorbidityServlet> computeComorbidityServletRegistration1() {

diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
@@ -8,7 +8,7 @@ spring.freemarker.suffix=.ftl
 spring.freemarker.template-loader-path=classpath:/wtempl/,classpath:/retempl/
 
 spring.servlet.multipart.enabled=true
-spring.servlet.multipart.location=/home/ronzano/comorbidity4web/tmp
+spring.servlet.multipart.location=/path/to/temporary/files/directory
 spring.servlet.multipart.max-file-size=1000MB
 spring.servlet.multipart.max-request-size=1000MB